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Monday 20th July 2009 : "Bibliographic Management meets Web 2.0" There are now several online tools for managing researchers' personal collections of scientific literature, from current awareness to bibliography production. Some of them are in the mould of traditional reference management software, but others started out as Web 2.0 applications. Examples include: Endnoteweb, RefWorks, Mendeley, Zotero, CiteULike, Connotea. This hands-on workshop will be a showcase for a number tools mentioned above to help scientific researchers, looking at future possibilities for managing literature in the cloud. If you wish to join us or ask any questions regarding these products, leave a message in this room.
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Mike Chelen
Fwd: Which reference management software uses fields formatted (PMID:12473109) in the text to format refs and the biblio, please? (via
Mike Chelen
Open-Access-Statistics project DINI - Deutsche Initiative für Netzwerkinformation -
Open-Access-Statistics project DINI - Deutsche Initiative für Netzwerkinformation
"Scientific Publications cover a wide variety of publishers, hosts, business models, usage models, publication stages, logical and technical presentation. Therefore it is important to learn which portions of the publication space can be and which agents want to be included in the sampling. For those willing to participate only two aspects are relevant: 1. What data needs to be gathered? 2. How can it be transferred to the statistics provider? Open-Access-Statistics (OA-S) is a joint project adressing these questions. Starting in July 2008 an infrastructure for the standardised accumulation of heterogenous web log data with an emphasis on institutional repositories will be built. In tight cooperation with the Network of Open Access Repositories (OA-N) various added value services will be made available to users." - Mike Chelen from Bookmarklet
What D said. - Bill Hooker
Won't load for me at the moment. - Bill Hooker
Completed the questionnaire, provided links to things like, OpenID, friendfeed, etc. Have to say, though, that some of the questions were worded somewhat unclearly. - Mr. Gunn
D0r0th34: thrilled to see existing and ongoing exploration of the topic, which is a natural extension for scholarly repositories and a crucial goal for ongoing curation. now reading one of the linked papers, "Open Access Statistics: an examination how to generate interoperable usage information from distributed open access services" (Herb, Ulrich '09) - Mike Chelen
Nathalie Cornee
Free Online Tools Simplify Research: Zotero and iCyte « ResourceShelf -
Frank Norman
Innovations in Reference Management - on 14th January 2010, at Kents Hill in Milton Keynes.
Mike Chelen
"A place to share information about Article-level metrics." - Mike Chelen from Bookmarklet
Great initiative ;-) - io2a
exciting to see how many new and interesting posts there are on the topic ^_^ - Mike Chelen
Mike Chelen
"Links any Document Object Identifiers for resolution with" - Mike Chelen from Bookmarklet
currently works with plaintext DOIs like and with DOI class spans like - Mike Chelen
RegExp missing some chars, e.g., % if URL-encoded. We tend to use 10\.(?:\d{4})/(?:[^ "'<&]+) but that can break too - it's annoying that the DOI spec doesn't limit the chars allowed! This is for searching the whole text (incl. within href), not element-wise so might not suit your code exactly. - Fergus Gallagher
Fergus: going to take a look and give that a try, probably only will try to work with displayed text, but it might be cool to add compatibility with any kind of field attribute or xhtml. thanks! - Mike Chelen
One special case worth looking for is "COiNS" OpenURL. Our (jQuery) code is var z = jQuery(".Z3988:eq(0)"); if (z.length) { var r = z.attr("title").split("&"); for (var i=0; i<r.length; i++) { var x = decodeURIComponent(r[i]); if (/^rft_id=info:doi\/.*?(10\.\d\d\d\d\/.*)/.exec(x)) { var doi = RegExp.$1; doSomething(doi); return; } } } - Fergus Gallagher
Mike Chelen
access PLoS article level metrics by DOI for use in Javascript and more - Mike Chelen
Mike Chelen
Re: tasks overview wishlist: Canonical citing reference [Debian Science] -
"Dear all, last year, Michael opened a discussion to have bibliographic information displayed in package summaries: In the discussion that followed, we talked about where to store this information, and in which format, since adding more content to the debian/control file is not an easy thing (it ‘costs’ a lot because it goes to pivotal files like the Packages.gz files on our mirrors). A four line summary is available here: This year, some progresses are being made. For the display, Andreas has modified the ‘Web sentinels’ so that they can display bibliographic informations. See for instance. But currently the limitation of the system is that the bibliographic information is in a quite remote location, in the Blends ‘tasks’ files. I am currently working on a new workflow which would help the... more... - Mike Chelen from Bookmarklet
Mike Chelen
Mike Chelen
PLoS articles by citation type, journal and publication year: 2009, 2008, and earlier sharp contrast #plosalm #manyeyes #visualization #original -
see which journals received each type of citation (scopus, crossref, and pubmed) and compare among the most recent years - Mike Chelen
Mike Chelen
Experimental PLoS ALM import to Drupal with Node Import, CCK and Faceted Search -
Drupal CCK node types are available at and CSV formatted data at - Mike Chelen from Bookmarklet
The goal is to help people find answers to questions about the data through a web interface. For example, to see which non-research article from PLoS Biology in 2008 has the highest rate of citations: . Then hopefully to make the results available as XML, JSON and more. - Mike Chelen
XML or JSON would be fun since the results could be pulled into graphic APIs like Google Charts - Mike Chelen
Mike - this is exactly the type of thing we are hoping people will start doing with this data. Let me know how we can help! - Peter Binfield
Peter: with so much useful data, seeing everything done with it is exciting. a filtered search has been implemented (uses CCK and Views) with the results now available as RSS. more frequently updated source data would definitely be helpful for everyone interested in the latest information, thanks! - Mike Chelen
Raw XML is now available, change the url from rss.xml to raw.xml with any RSS feed from the advanced search. For example:... more... - Mike Chelen
Mike - in the next couple of weeks we will add all the 'missing' usage data (pre-July 05 and 1st 200 PLoS ONE articles). I will ping you when we have it in an excel sheet. - Peter Binfield
Mike Chelen : Visualizing information flow in science - : Visualizing information flow in science : Visualizing information flow in science
Show all
"Interactive visualizations based on the Eigenfactor™ Metrics and hierarchical clustering to explore emerging patterns in citation networks." - Mike Chelen from Bookmarklet
Mike Chelen
"The OpenSearch service provides a structured resource discovery facility for content hosted on" - Mike Chelen from Bookmarklet
Mike Chelen
Mike Chelen
PLoS article title and citation count visualizations with Many Eyes #plosalm #manyeyes #visualization #original
Show all
yeah ibm manyeyes is pretty cool i must concur complex complicated and ultra geeky - Robert Higgins
The chart types and options are pretty flexible, and some are interactive: Phrase Net Wordle Scatterplot - Mike Chelen
Mike Chelen
"Takes a doi as input and searches PubMed. Returns the PubMed id if a corresponding one exists. Returns nothing if one does not exist." - Mike Chelen from Bookmarklet
Mike Chelen
"BibApp matches researchers on your campus with their publication data and mines that data to see collaborations and to find experts in research areas." - Mike Chelen from Bookmarklet
Nathalie Cornee
citeulike and mendeley collaborate -
Frank Norman
PLoS Comp Biol article on defrosting digital libs
Mike Chelen
Zotero Blog » Follow Libraries and Collections with Feeds -
Zotero Blog » Follow Libraries and Collections with Feeds
"Anyone with a feed reader can now follow public Zotero libraries simply by clicking the feed icon at the right-hand side of the browser address bar. Feeds are generated at the library and collection level, and for group libraries as well as individual libraries." - Mike Chelen from Bookmarklet
Martin Fenner
CiteULike + BibDesk: Sync your references and live smarter: - Nathalie Cornee
CiteULike Plugin Developer's Kit - - Nathalie Cornee
CiteULike traffic stats - - Nathalie Cornee
CiteULike: Interview with Kevin Emamy - - Martin Fenner
Kevin Emamy talks about CiteULike - Martin Fenner
CiteULike is totally Web-based. I haven't decided yet whether I prefer the web-only approach (Refworks, CiteULike, Connotea) or the web/desktop combo approach (Endnote, Mendeley, Zotero). - Martin Fenner
CiteULike allows PDF uploads. File can only be downloaded by user and private groups. - Martin Fenner
Importing references into Connotea and CiteULike appears to be easier (and faster) than with Endnoteweb and Refworks. - Martin Fenner
Kevin talks about how CiteUlike helps users discover interesting references that they otherwise wouldn't have found. - Martin Fenner
indeed, it's easy to search keywords in citeulike and retrieve other users who have used these tags previously - Nathalie Cornee
Tags and users allow the discovery of interesting related papers. - Martin Fenner
12 citation styles cover 90% of uses, so CiteUlike focussed on those. - Martin Fenner
You can drag & drop citations (in your preferred style) into your word processor document, or you export references as ris or rtf. - Martin Fenner
Other social features of CiteULike: connections, neighbours, and zeitgeist. Neighbours are users that have similar references in their library. Zeitgeist shows you the most popular references over a period of time (e.g. the last 7 days). - Martin Fenner
Kevin shows how PLoS articles have a link to CiteULike (showing the number of users tagging that article in CiteULike). - Martin Fenner
Kevin talks about the business model for a service such as CiteULike. The revenue from advertising alone would not be sufficient. Sponsorship by Springer is major source of income. - Martin Fenner
Really interesting to see the differences in what features are seen as important between Endnoteweb/Refworks and Connotea/CiteULike. - Martin Fenner
I like the CiteGeist feature, and not just because of the terrible pun! - Frank Norman
Interesting social features too - connections (like friends), messages, neighbours, groups. - Frank Norman
To get the bookmarklet to work for PubMed you need to get article URL in browser address bar, before clicking on the "Post to CiteuLike" button - Patti Biggs
Neither of the social bookmarking tools (CiteuLike or Connotea) allow for formatted text, accented characters etc in article titles, author titles - Patti Biggs
Accented chars? Yes we (citeulike) do that. Formatted text too as long as source and output formats compatible. - Fergus Gallagher
But does it capture greek, italic and superscripts from the source? - Frank Norman
I thought so - examples? - Fergus Gallagher
Ah, just realised that the presentations yesterday were all using Pubmed as their source, so wouldn't have a chance of capturing anything except plain text. I'll check this out later. - Frank Norman
Martin Fenner
recent presentation of Mendeley available at - Nathalie Cornee
Interview with Victor Henning from Mendeley (from Martin Fenner): - Nathalie Cornee
Victor Henning starts Mendeley presentation. - Martin Fenner
Software still in beta, much younger than the other tools presented in the workshop. Version 1.0 sometime later this year. - Martin Fenner
Desktop client plus online tools - Frank Norman
Import of references using bookmarklet. - Martin Fenner
simply drag pdf documents to a ref (it finds duplicates, keywords, doi) - Nathalie Cornee
Fulltext search, notes and highlighted text in PDF documents. - Martin Fenner
Mendeley makes it easier (compared to Connotea and CiteULike) to import more than one document of say a PubMed search. - Martin Fenner
user- friendly tool - Nathalie Cornee
Fulltext search of PDF files both in the Web and Desktop version of Mendeley. - Martin Fenner
Setting of syncing of PDF files in Mendeley: no files, files from selected collections, all files. You have to set up private groups for file sharing, no anonymous filesharing. - Martin Fenner
Mendeley can automatically rename PDF files (e.g. author, journal, year). Option of first author only would be nice. - Martin Fenner
Public collections in Mendeley possible (without PDF files). Can be embedded in other web pages, great for lab web pages. You can subscribe to public collections. Public collections will soon also be available as RSS feeds. - Martin Fenner
Dashboard gives you new information (e.g. profile updates) of your contacts. - Martin Fenner
Mendeley Desktop has default "My publications" folder to put in all the papers you authored. - Martin Fenner
You have to switch back and forth between Mendeley Desktop and Microsoft Word to insert citations. No small popup window as with the other tools. - Martin Fenner
Shared groups in Mendeley are great to co-author a paper. - Martin Fenner
Mendeley and CiteULike integrated since April. Next Mendeley release will allow the same synchronization with Zotero. - Martin Fenner
40.000 documents are added to Mendeley every day, database is doubling every 7 weeks. Once more documents are added, it will be interesting to look at usage statistics. These will be the basis for reading recommendations. - Martin Fenner
"You have to switch back and forth between Mendeley Desktop and Microsoft Word to insert citations." - Martin, I was under the impression there was an integrated toolbar for Word? Could you ask? - Heather
I've been thinking about a journal club service (manage members and assign papers/dates) in conjunction with Mendeley and maybe PLoS One (JC coverage as post-publication data/review statistics). Is this a good idea? - Björn Brembs
Heather, there is a toolbar, but clicking on "insert citation" there opens up Mendeley Desktop. - Martin Fenner
Bjoern, yes I think so! Passed in on to Jan and Victor standing next to me. - Martin Fenner
Thanks! I luuuuuuuurve the PDF import thing. Next fall I promise to organize into groups that I will finally share. - Heather
File renaming = ok, but what about reading/writing xmp metadata? The more interchange we'll have between bib apps,repositories etc. the more usefull this Standard will become. - Lambert Heller from iPhone
@Björn: yepp! - Claudia Koltzenburg
Frank Norman
Magisterial overview from Martin Fenner - summation of the day
Who is using what? Most at the workshop are using Endnote/endnoteweb, Ref Man. A few votes each for Refworks, Papers, connotea, citeulike, Zotero - Frank Norman
Is there a perfect tool for everything? No! Different tools have different functionalities and compatibilities - Frank Norman
What did we learn today? Products develop quickly. If product X seems inadequate today, it may be much better in 6 months. (By which time there will be another 1 or 2 new products!) - Frank Norman
I must agree, Martin did an amazing job liveblogging the event. Will keep an eye open for his write up of the meeting. - Ricardo Vidal
is cost important? Do you trust soft which are free? - Nathalie Cornee
How do librarians offer advice here? We need to know about the different capabilities in case people ask us for advice/support - Frank Norman
We have to be user-driven and not proscriptive. - Frank Norman
Will these tools work OK with research data? We will need to manage research data better in future - Frank Norman
There's a comparison chart here that is a starting point: - Patti Biggs
Collaboration between tools is seen as a positive step (e.g. Mendeley with citeulike and with Zotero) - Frank Norman
What tool to use? What you've always used, or switch to something else if existing tool doesn't meet all needs (e.g. to free you from being tied to desktop) - Frank Norman
Tools need to integrate with your favourite bib database. And to integrate with other team memebrs' tools. And with local support offerings - Frank Norman
Portability (mobility) is a key requirement. - Frank Norman
What did the presenters learn today? Realised it's hard for users to abandon legacy tools. Many users do use multiple tools. - Frank Norman
Hence new tool developers try to integrate and collaborate - Frank Norman
Librarians sometimes have a different use case than end-user - take account of broad institutional needs and realities. Developers should be aware of librarians' role/input - Frank Norman
The best tool? - it is not a sensible question to ask. - Frank Norman
In addition to Martin's overview: - Rintze Zelle
Greek characters, italics, rich text are still not well handled - Frank Norman
THE END! (but keep on discussing and questioning) - Frank Norman
Martin Fenner
Biobliographic Management meets Web 2.0 - Discussion
Any questions you want to have addressed in the discussion? - Martin Fenner
Martin Fenner
7 things you should know about zotero - - Nathalie Cornee
Zotero: Interview with Trevor Owens - - Martin Fenner
Rintze Zelle talks about Zotero - Martin Fenner
Zotero can save more than one item from a webpage and directly import associated PDF files (different from Connotea and CiteULike), it depends on translators for that. - Martin Fenner
Zotero can add items by identifier (DOI, PMID or ISBN). - Martin Fenner
Zotero translators are powerful tools, seem to be smarter than some of the bookmarklets of the other tools. - Martin Fenner
zotero main library always contains all references (even if it's got subfolders) - Nathalie Cornee
Interestingly, Zotero uses folders and tags (they overlap in functionality). Also subfolders and smart folders (i.e. saved searches). - Martin Fenner
Zotero does fulltext search of PDF files stored in the library. - Martin Fenner
Zotero 2.0 beta syncs your local library with the Zotero server and allows for sharing of your references. - Martin Fenner
Mendeley Word plugin interferes with both the Endnoteweb and Zotero plugins. - Martin Fenner
Zotero ships with about 20 default citation styles. 2000 additional styles (using the CSL format) can be installed. The styles can't be edited by the average user (tool for that is in the works). - Martin Fenner
Zotero Word plugin doesn't work well with the "track changes" feature of Microsoft Word. - Martin Fenner
Zotero doesn't support rich text in citations. - Martin Fenner
Zotero 2.0 release version expected in a few months. Zotero 2.0 beta works fine, but syncing feature not ready for release yet. - Martin Fenner
Like the fact that you can save search strategies to use again - very useful as library gets larger - Patti Biggs
Nathalie Cornee
J Med Libr Assoc. 2004 January; 92(1): 111–113. Refworks - - Nathalie Cornee
a brief review of refworks - - Nathalie Cornee
Aaron Maierhofer talks about Refworks. - Martin Fenner
References are usually imported via bookmarklet, but direct search of many databases also possible. - Martin Fenner
"Global Edit" to add/modify/delete many references at once. - Martin Fenner
refworks manages pdf files - Nathalie Cornee
Fulltext PDF files of references have to be downloaded, then attached to the reference. - Martin Fenner
Refworks allows sharing of references (individual folders or all references). Sharing has many options, I like the RSS feed of 10 most recently added references. Sharing works via secret URL, no Refworks license or password necessary. - Martin Fenner
Write-N-Cite Refworks plugin for Windows works offline, but currently read-only. - Martin Fenner
Attachment options (i.e. whether or not to allow sharing of PDF files) in Refworks can be customized by the institution. - Martin Fenner
Refworks allows direct search of many databases using Z39.50 protocol. - Martin Fenner
Refworks requires an institutional license. - Martin Fenner
many fields such as authors, sources are hyperlinked - Nathalie Cornee
Refworks allows fulltext search of txt and pdf attachments. - Martin Fenner
What about a "Shared Area" with public references from all users, across Campus borders? Maierhofer mentioned that idea in a talk at HU Berlin ca 2 years ago. - Lambert Heller from iPhone
Can have italics in records in Refworks - Patti Biggs
Dear Mr. Heller, yes I remember our conversation in Berlin. This is still on our agenda.I will contact you off-line to give you an update. Can you please send me your current email address, as the one I have does not seem to work anymore? - Frank Norman
Nathalie Cornee
manufacturer comparison of endnoteweb & endnote - - Nathalie Cornee
Presentation by Stephanie Marshall - Martin Fenner
EndnoteWeb doesn't have all the features of the desktop package, and this may stay like this. - Martin Fenner
Endnoteweb can import web pages using a bookmarklet. - Martin Fenner
Bulk importing from Google Scholar is difficult, because the database is not as structured as PubMed, Scopus or Web of Science. - Martin Fenner
Google Scholar import into Endnoteweb via export/import of .ris file, one reference at a time. - Martin Fenner
updated every 3 months - Nathalie Cornee
Endnoteweb allows sharing of references with other Endnoteweb users. You use email addresses for that. - Martin Fenner
Differences between Endnoteweb and Endnote: more than 10.000 references possible, PDF management, connection files can be customized. - Martin Fenner
Endnoteweb not sold as a single product, need a site license or Endnote Desktop. - Martin Fenner
I'm seeing a conflict with Mendeley when using the Endnoteweb Word plugin - Frank Norman
Also conflict with Zotero with RIS export earlier on. - Martin Fenner
not possible to add pdf files yet - Nathalie Cornee
Apparently the default reference type when you import from Google Scholar is "ancient text". Changing this improves it a bit - Frank Norman
Nathalie Cornee
Connotea: Saving References Made Simple - - Nathalie Cornee
Grace Barnes talks about Connotea - Martin Fenner
emphasis on sharing references + integrates with other more "traditional" bib ref tools - Nathalie Cornee
Focus of Connotea is more on sharing and social bookmarking. Is intented to work together with more traditional reference management tools. - Martin Fenner
by default, libraries are all shared (unless you specify to make yours private) - Nathalie Cornee
No easy way in Connotea to import a list of references from PubMed at once. Either import one by one using the bookmarklet or import/export using ris. - Martin Fenner
"Connotea is currently under a very high load. Please try again in a few seconds." - Martin Fenner
Connotea does not allow PDF management. One reason: Connotea is a tool from a publisher (Nature Publishing Group). - Martin Fenner
Different tool required to put references in a manuscript, but Connotea exports to Bibtex and Word 2007 Bibliography formats. - Martin Fenner
Can only have one URL per reference - Frank Norman
When saving references from PubMed need to have an individual record URL in address bar or will try to bookmark the PubMed homepage - Patti Biggs
Can see others who have bookmarked same page, so develop a community with similar interests - Patti Biggs
Nathalie Cornee
endnoteweb limited to 10000 references (desktop version is unlimited)
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